GSE104921
Signal integration in lymphocytes via convergent genomic actions of NFATs with IRF4 and  IRF8
Lymphocyte activation and effector state differentiation critically depend on integration of  multiple signals, including those from antigen, co-stimulatory ligand and cytokine receptors.  Thus, discovery of molecular components and mechanisms underlying signal integration is vital  for the understanding and control of adaptive immune responses. Stimulation of antigen  receptors in lymphocytes leads to the activation of NFAT family transcription factors (TFs) as  well as the inducible expression of the immune-selective IRFs, IRF4 and IRF8; the latter are  differentially controlled by co-stimulatory ligand and cytokine receptor signaling. Despite their  major overlapping functions in lymphocyte activation and differentiation, it has remained  enigmatic if NFATs can perform signal integration with IRF4 and IRF8, via their cooperative  assembly on composite genomic regulatory elements. Composite elements (CEs) provide a  powerful means of signal integration by inducible TFs and despite their clear importance, CEs  arguably remain the least explored elements within cis-regulomes. To test the above  hypothesis, we deployed a generalizable computational strategy, which revealed a stereospecific  NFAT-IRF composite element (NICE) motif that was enriched within active chromatin regions  (H3K27Ac) of activated B and T lymphocytes. NICE containing DNA sequences promoted  cooperative binding of NFATs with IRF4 or IRF8. Genomic analyses in activated B cells  revealed co-dependent genes that undergo activation or repression and contain NICE motifs in  their regulatory regions. Notably, NFATc2 and IRF8 form a positive feedforward loop and  coordinately repress the Prdm1 gene by binding a NICE motif in a phylogenetically conserved  region, thereby inhibiting extrafollicular plasma cell differentiation and promoting the germinal  center fate of activated B cells. The NICE motif is also enriched in DNA sequences located in  accessible chromatin of human lymphocytes, suggesting evolutionary conservation of its  function. The cooperative assembly of NFAT family members with IRF4 and IRF8 on NICE  motifs reveals a new genomic control mechanism that enables signal integration during  lymphocyte activation and differentiation. Overall design: For ChIP-Seq, B  cells were stimulated with F(ab') 2 fragment goat anti–mouse IgM, a-CD40, IL-2,IL-4 and IL-5. Naïve CD4 T cells were stimulated with plate coated a-CD3 and a-CD28.  Human T cells were stimulated with anti-CD3/28 beads. For RNA-seq, B cells were stimulated in the absence or presence of 11R-VIVT.